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- PDB-6dhn: Bovine glutamate dehydrogenase complexed with Eu3+ -

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Basic information

Entry
Database: PDB / ID: 6dhn
TitleBovine glutamate dehydrogenase complexed with Eu3+
ComponentsGlutamate dehydrogenase 1, mitochondrial
KeywordsOXIDOREDUCTASE / Europium / glutamate / dehydrogenase
Function / homology
Function and homology information


Glutamate and glutamine metabolism / Transcriptional activation of mitochondrial biogenesis / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / glutamine metabolic process / positive regulation of insulin secretion ...Glutamate and glutamine metabolism / Transcriptional activation of mitochondrial biogenesis / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / glutamine metabolic process / positive regulation of insulin secretion / mitochondrial inner membrane / mitochondrial matrix / GTP binding / endoplasmic reticulum / mitochondrion / ATP binding / identical protein binding
Similarity search - Function
Helix Hairpins - #140 / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal ...Helix Hairpins - #140 / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / Helix Hairpins / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / GUANOSINE-5'-TRIPHOSPHATE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Glutamate dehydrogenase 1, mitochondrial / Glutamate dehydrogenase 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSmith, T.J.
CitationJournal: FEBS J. / Year: 2011
Title: A novel mechanism of V-type zinc inhibition of glutamate dehydrogenase results from disruption of subunit interactions necessary for efficient catalysis.
Authors: Bailey, J. / Powell, L. / Sinanan, L. / Neal, J. / Li, M. / Smith, T. / Bell, E.
History
DepositionMay 20, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionJul 25, 2018ID: 3MVO
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate dehydrogenase 1, mitochondrial
B: Glutamate dehydrogenase 1, mitochondrial
C: Glutamate dehydrogenase 1, mitochondrial
D: Glutamate dehydrogenase 1, mitochondrial
E: Glutamate dehydrogenase 1, mitochondrial
F: Glutamate dehydrogenase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,95530
Polymers382,9486
Non-polymers12,00724
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, It is well established that the active unit is a hexamer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51510 Å2
ΔGint-209 kcal/mol
Surface area94180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.110, 98.760, 165.640
Angle α, β, γ (deg.)90.00, 101.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain A and (resid 1 through 2 or resid 4...
211(chain B and (resid 1 through 2 or resid 4...
311(chain C and (resid 1 through 2 or resid 4...
411(chain D and (resid 1 through 2 or resid 4...
511(chain E and (resid 1 through 2 or resid 4...
611(chain F and (resid 1 through 2 or resid 4...

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Components

#1: Protein
Glutamate dehydrogenase 1, mitochondrial /


Mass: 63824.699 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: A0A140T871, UniProt: P00366*PLUS, glutamate dehydrogenase
#2: Chemical
ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H29N7O14P2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 8% PEG8000, 0.15 M sodium chloride, 5% MPD, 0.1 M triethanolamine-HCl, pH 7.0, 50 mM monosodium glutamate, 2 mM GTP, 2 mM NADPH, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Sep 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 60196 / % possible obs: 96.3 % / Redundancy: 2.5 % / Net I/σ(I): 4.2
Reflection shellResolution: 3.3→3.45 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→43.888 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 29.48
RfactorNum. reflection% reflection
Rfree0.3014 2712 5.07 %
Rwork0.2597 --
obs0.2618 53467 92.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→43.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23496 0 780 0 24276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01124834
X-RAY DIFFRACTIONf_angle_d1.7833654
X-RAY DIFFRACTIONf_dihedral_angle_d8.07914640
X-RAY DIFFRACTIONf_chiral_restr0.1263630
X-RAY DIFFRACTIONf_plane_restr0.0154290
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3615X-RAY DIFFRACTIONPOSITIONAL
12B3615X-RAY DIFFRACTIONPOSITIONAL0.14
13C3615X-RAY DIFFRACTIONPOSITIONAL0.112
14D3615X-RAY DIFFRACTIONPOSITIONAL0.13
15E3615X-RAY DIFFRACTIONPOSITIONAL0.136
16F3615X-RAY DIFFRACTIONPOSITIONAL0.15
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.360.37941520.33122587X-RAY DIFFRACTION91
3.36-3.42460.34541240.3242598X-RAY DIFFRACTION91
3.4246-3.49450.36221280.30542638X-RAY DIFFRACTION91
3.4945-3.57040.35681270.30172646X-RAY DIFFRACTION91
3.5704-3.65340.31041460.29142622X-RAY DIFFRACTION91
3.6534-3.74480.31841380.26692606X-RAY DIFFRACTION91
3.7448-3.8460.311530.27012691X-RAY DIFFRACTION93
3.846-3.95910.31161300.25352685X-RAY DIFFRACTION92
3.9591-4.08680.27041340.25642670X-RAY DIFFRACTION92
4.0868-4.23270.29381580.25562633X-RAY DIFFRACTION92
4.2327-4.4020.30751420.25182668X-RAY DIFFRACTION92
4.402-4.60220.27331320.2322721X-RAY DIFFRACTION93
4.6022-4.84450.28961700.2332710X-RAY DIFFRACTION94
4.8445-5.14760.30761490.23392694X-RAY DIFFRACTION94
5.1476-5.54430.28991500.24152696X-RAY DIFFRACTION93
5.5443-6.1010.25541380.24662737X-RAY DIFFRACTION94
6.101-6.98070.28341660.2442739X-RAY DIFFRACTION94
6.9807-8.78340.24921510.22182746X-RAY DIFFRACTION94
8.7834-43.89220.28361240.24252668X-RAY DIFFRACTION88

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